#:use-module (guix download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
+ #:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.16.0")
+ (version "1.16.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "014h2q346ynfdbpavh4p69cyv4j65hk934liq5892zznjzl73z7p"))))
+ "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.16.1")
+ (version "3.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
+ "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
("r-biocmanager" ,r-biocmanager)
- ("r-biostrings" ,r-biostrings)
- ("r-delayedarray" ,r-delayedarray)
- ("r-go-db" ,r-go-db)
("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
+ ("r-dbi" ,r-dbi)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-ensembldb" ,r-ensembldb)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
- ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-go-db" ,r-go-db)
+ ("r-graph" ,r-graph)
+ ("r-idr" ,r-idr)
("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-annotationdbi" ,r-annotationdbi)
("r-limma" ,r-limma)
+ ("r-matrixstats" ,r-matrixstats)
("r-multtest" ,r-multtest)
("r-rbgl" ,r-rbgl)
- ("r-graph" ,r-graph)
("r-regioner" ,r-regioner)
- ("r-dbi" ,r-dbi)
- ("r-ensembldb" ,r-ensembldb)
- ("r-biobase" ,r-biobase)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-seqinr" ,r-seqinr)
- ("r-idr" ,r-idr)
- ("r-genomicalignments" ,r-genomicalignments)
("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-rsamtools" ,r-rsamtools)
("r-venndiagram" ,r-venndiagram)))
(home-page "http://bioconductor.org/packages/ChIPpeakAnno")
(synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
(home-page "http://bioconductor.org/packages/marray")
(synopsis "Exploratory analysis for two-color spotted microarray data")
(description "This package contains class definitions for two-color spotted
-microarray data. It also includes fuctions for data input, diagnostic plots,
+microarray data. It also includes functions for data input, diagnostic plots,
normalization and quality checking.")
(license license:lgpl2.0+)))
(home-page "https://bioconductor.org/packages/InteractionSet")
(synopsis "Base classes for storing genomic interaction data")
(description
- "This packages provides the @code{GInteractions},
+ "This package provides the @code{GInteractions},
@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
experiments.")
(define-public r-icobra
(package
(name "r-icobra")
- (version "1.12.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "iCOBRA" version))
(sha256
(base32
- "1w9frnczgypzc2czbwrvlizqcqhbp6cdpyws7vkmnn9k0ggzxvfc"))))
+ "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
(properties `((upstream-name . "iCOBRA")))
(build-system r-build-system)
(propagated-inputs
(synopsis "Analysis of translational activity")
(description
"Genome wide studies of translational control is emerging as a tool to
-study verious biological conditions. The output from such analysis is both
+study various biological conditions. The output from such analysis is both
the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
involved in translation (the actively translating mRNA level) for each mRNA.
The standard analysis of such data strives towards identifying differential
actively translated mRNA levels that are independent of underlying differences
in cytosolic mRNA levels. This package allows for such analysis using partial
variances and the random variance model. As 10s of thousands of mRNAs are
-analyzed in parallell the library performs a number of tests to assure that
+analyzed in parallel the library performs a number of tests to assure that
the data set is suitable for such analysis.")
(license license:gpl3)))
(define-public r-dose
(package
(name "r-dose")
- (version "3.10.0")
+ (version "3.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DOSE" version))
(sha256
(base32
- "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv"))))
+ "0ab7mgj42fg6608qkciyqivr1n8s8r5ibvp0z3jfclrnyx6cl0w1"))))
(properties `((upstream-name . "DOSE")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rgadem
(package
(name "r-rgadem")
- (version "2.31.0")
+ (version "2.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGADEM" version))
(sha256
(base32
- "0mck3dsxzjxszfs1cl96kd83q7n85p3763s0y3gwws69jn7p6w5j"))))
+ "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
(properties `((upstream-name . "rGADEM")))
(build-system r-build-system)
(propagated-inputs
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
- (version "1.8.0")
+ (version "1.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
- "03f130vcd6hd3fv2pg60id0ddd6qkwsyx73gm907xaayf42ar2pj"))))
+ "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
(define-public r-aucell
(package
(name "r-aucell")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AUCell" version))
(sha256
(base32
- "025q1as9pifbxa7hidlz634q6d7l73zx8mqy4rjbfrk7d5615xvm"))))
+ "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
(properties `((upstream-name . "AUCell")))
(build-system r-build-system)
(propagated-inputs
(define-public r-massspecwavelet
(package
(name "r-massspecwavelet")
- (version "1.48.1")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MassSpecWavelet" version))
(sha256
(base32
- "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz"))))
+ "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
(properties
`((upstream-name . "MassSpecWavelet")))
(build-system r-build-system)
(define-public r-xcms
(package
(name "r-xcms")
- (version "3.4.4")
+ (version "3.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "xcms" version))
(sha256
(base32
- "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww"))))
+ "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-wrench
(package
(name "r-wrench")
- (version "1.0.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Wrench" version))
(sha256
(base32
- "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg"))))
+ "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
(properties `((upstream-name . "Wrench")))
(build-system r-build-system)
(propagated-inputs
(define-public r-wiggleplotr
(package
(name "r-wiggleplotr")
- (version "1.6.1")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wiggleplotr" version))
(sha256
(base32
- "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3"))))
+ "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
(define-public r-widgettools
(package
(name "r-widgettools")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "widgetTools" version))
(sha256
(base32
- "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf"))))
+ "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
(properties `((upstream-name . "widgetTools")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/widgetTools/")
(synopsis "Tools for creating interactive tcltk widgets")
(description
- "This packages contains tools to support the construction of tcltk
+ "This package contains tools to support the construction of tcltk
widgets in R.")
;; Any version of the LGPL.
(license license:lgpl3+)))
(define-public r-webbioc
(package
(name "r-webbioc")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "webbioc" version))
(sha256
(base32
- "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi"))))
+ "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
(build-system r-build-system)
(inputs
`(("netpbm" ,netpbm)
(define-public r-zfpkm
(package
(name "r-zfpkm")
- (version "1.4.1")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "zFPKM" version))
(sha256
(base32
- "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5"))))
+ "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
(properties `((upstream-name . "zFPKM")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rbowtie2
(package
(name "r-rbowtie2")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rbowtie2" version))
(sha256
(base32
- "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr"))))
+ "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
(properties `((upstream-name . "Rbowtie2")))
(build-system r-build-system)
(inputs
(define-public r-progeny
(package
(name "r-progeny")
- (version "1.4.1")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "progeny" version))
(sha256
(base32
- "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7"))))
+ "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
(build-system r-build-system)
(propagated-inputs `(("r-biobase" ,r-biobase)))
(home-page "https://github.com/saezlab/progeny")
(define-public r-arrmnormalization
(package
(name "r-arrmnormalization")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ARRmNormalization" version))
(sha256
(base32
- "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd"))))
+ "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
(properties
`((upstream-name . "ARRmNormalization")))
(build-system r-build-system)
custom Txdb objects) that are costly or difficult to create, web resources,
and data files used across sessions.")
(license license:artistic2.0)))
+
+(define-public r-iclusterplus
+ (package
+ (name "r-iclusterplus")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "iClusterPlus" version))
+ (sha256
+ (base32
+ "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
+ (properties `((upstream-name . "iClusterPlus")))
+ (build-system r-build-system)
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://bioconductor.org/packages/iClusterPlus/")
+ (synopsis "Integrative clustering of multi-type genomic data")
+ (description
+ "iClusterPlus is developed for integrative clustering analysis of
+multi-type genomic data and is an enhanced version of iCluster proposed and
+developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
+from the experiments where biological samples (e.g. tumor samples) are
+analyzed by multiple techniques, for instance, @dfn{array comparative genomic
+hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
+on. In the iClusterPlus model, binary observations such as somatic mutation
+are modeled as Binomial processes; categorical observations such as copy
+number states are realizations of Multinomial random variables; counts are
+modeled as Poisson random processes; and continuous measures are modeled by
+Gaussian distributions.")
+ (license license:gpl2+)))
+
+(define-public r-rbowtie
+ (package
+ (name "r-rbowtie")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rbowtie" version))
+ (sha256
+ (base32
+ "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
+ (properties `((upstream-name . "Rbowtie")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://bioconductor.org/packages/Rbowtie/")
+ (synopsis "R bowtie wrapper")
+ (description
+ "This package provides an R wrapper around the popular bowtie short read
+aligner and around SpliceMap, a de novo splice junction discovery and
+alignment tool.")
+ (license license:artistic2.0)))
+
+(define-public r-sgseq
+ (package
+ (name "r-sgseq")
+ (version "1.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "SGSeq" version))
+ (sha256
+ (base32
+ "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
+ (properties `((upstream-name . "SGSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-igraph" ,r-igraph)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-runit" ,r-runit)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/SGSeq/")
+ (synopsis "Splice event prediction and quantification from RNA-seq data")
+ (description
+ "SGSeq is a package for analyzing splice events from RNA-seq data. Input
+data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
+represented as a splice graph, which can be obtained from existing annotation
+or predicted from the mapped sequence reads. Splice events are identified
+from the graph and are quantified locally using structurally compatible reads
+at the start or end of each splice variant. The software includes functions
+for splice event prediction, quantification, visualization and
+interpretation.")
+ (license license:artistic2.0)))
+
+(define-public r-rhisat2
+ (package
+ (name "r-rhisat2")
+ (version "1.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhisat2" version))
+ (sha256
+ (base32
+ "1y3zqvk1vbcb10r1myh6f5yzjvf7bhwhpiq78bs1k6spli4bzj0q"))))
+ (properties `((upstream-name . "Rhisat2")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("which" ,which)))
+ (propagated-inputs
+ `(("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-sgseq" ,r-sgseq)))
+ (home-page "https://github.com/fmicompbio/Rhisat2")
+ (synopsis "R Wrapper for HISAT2 sequence aligner")
+ (description
+ "This package provides an R interface to the HISAT2 spliced short-read
+aligner by Kim et al. (2015). The package contains wrapper functions to
+create a genome index and to perform the read alignment to the generated
+index.")
+ (license license:gpl3)))
+
+(define-public r-quasr
+ (package
+ (name "r-quasr")
+ (version "1.24.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "QuasR" version))
+ (sha256
+ (base32
+ "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
+ (properties `((upstream-name . "QuasR")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rbowtie" ,r-rbowtie)
+ ("r-rhisat2" ,r-rhisat2)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shortread" ,r-shortread)))
+ (home-page "https://bioconductor.org/packages/QuasR/")
+ (synopsis "Quantify and annotate short reads in R")
+ (description
+ "This package provides a framework for the quantification and analysis of
+short genomic reads. It covers a complete workflow starting from raw sequence
+reads, over creation of alignments and quality control plots, to the
+quantification of genomic regions of interest.")
+ (license license:gpl2)))
+
+(define-public r-rqc
+ (package
+ (name "r-rqc")
+ (version "1.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rqc" version))
+ (sha256
+ (base32
+ "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
+ (properties `((upstream-name . "Rqc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biocstyle" ,r-biocstyle)
+ ("r-biostrings" ,r-biostrings)
+ ("r-biovizbase" ,r-biovizbase)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-knitr" ,r-knitr)
+ ("r-markdown" ,r-markdown)
+ ("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-shortread" ,r-shortread)))
+ (home-page "https://github.com/labbcb/Rqc")
+ (synopsis "Quality control tool for high-throughput sequencing data")
+ (description
+ "Rqc is an optimized tool designed for quality control and assessment of
+high-throughput sequencing data. It performs parallel processing of entire
+files and produces a report which contains a set of high-resolution
+graphics.")
+ (license license:gpl2+)))
+
+(define-public r-birewire
+ (package
+ (name "r-birewire")
+ (version "3.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiRewire" version))
+ (sha256
+ (base32
+ "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
+ (properties `((upstream-name . "BiRewire")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)
+ ("r-slam" ,r-slam)
+ ("r-tsne" ,r-tsne)))
+ (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
+ (synopsis "Tools for randomization of bipartite graphs")
+ (description
+ "This package provides functions for bipartite network rewiring through N
+consecutive switching steps and for the computation of the minimal number of
+switching steps to be performed in order to maximise the dissimilarity with
+respect to the original network. It includes functions for the analysis of
+the introduced randomness across the switching steps and several other
+routines to analyse the resulting networks and their natural projections.")
+ (license license:gpl3)))
+
+(define-public r-birta
+ (package
+ (name "r-birta")
+ (version "1.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "birta" version))
+ (sha256
+ (base32
+ "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-limma" ,r-limma)
+ ("r-mass" ,r-mass)))
+ (home-page "https://bioconductor.org/packages/birta")
+ (synopsis "Bayesian inference of regulation of transcriptional activity")
+ (description
+ "Expression levels of mRNA molecules are regulated by different
+processes, comprising inhibition or activation by transcription factors and
+post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
+Inference of Regulation of Transcriptional Activity) uses the regulatory
+networks of transcription factors and miRNAs together with mRNA and miRNA
+expression data to predict switches in regulatory activity between two
+conditions. A Bayesian network is used to model the regulatory structure and
+Markov-Chain-Monte-Carlo is applied to sample the activity states.")
+ (license license:gpl2+)))
+
+(define-public r-ropls
+ (package
+ (name "r-ropls")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ropls" version))
+ (sha256
+ (base32
+ "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-biobase" ,r-biobase)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
+ (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
+ (synopsis "Multivariate analysis and feature selection of omics data")
+ (description
+ "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
+and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
+regression, classification, and feature selection of omics data where the
+number of variables exceeds the number of samples and with multicollinearity
+among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
+separately model the variation correlated (predictive) to the factor of
+interest and the uncorrelated (orthogonal) variation. While performing
+similarly to PLS, OPLS facilitates interpretation.
+
+This package provides imlementations of PCA, PLS, and OPLS for multivariate
+analysis and feature selection of omics data. In addition to scores, loadings
+and weights plots, the package provides metrics and graphics to determine the
+optimal number of components (e.g. with the R2 and Q2 coefficients), check the
+validity of the model by permutation testing, detect outliers, and perform
+feature selection (e.g. with Variable Importance in Projection or regression
+coefficients).")
+ (license license:cecill)))
+
+(define-public r-biosigner
+ (package
+ (name "r-biosigner")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biosigner" version))
+ (sha256
+ (base32
+ "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-e1071" ,r-e1071)
+ ("r-randomforest" ,r-randomforest)
+ ("r-ropls" ,r-ropls)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("pandoc" ,ghc-pandoc)
+ ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
+ (home-page "https://bioconductor.org/packages/biosigner/")
+ (synopsis "Signature discovery from omics data")
+ (description
+ "Feature selection is critical in omics data analysis to extract
+restricted and meaningful molecular signatures from complex and high-dimension
+data, and to build robust classifiers. This package implements a method to
+assess the relevance of the variables for the prediction performances of the
+classifier. The approach can be run in parallel with the PLS-DA, Random
+Forest, and SVM binary classifiers. The signatures and the corresponding
+'restricted' models are returned, enabling future predictions on new
+datasets.")
+ (license license:cecill)))
+
+(define-public r-annotatr
+ (package
+ (name "r-annotatr")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "annotatr" version))
+ (sha256
+ (base32
+ "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationhub" ,r-annotationhub)
+ ("r-dplyr" ,r-dplyr)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-readr" ,r-readr)
+ ("r-regioner" ,r-regioner)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/annotatr/")
+ (synopsis "Annotation of genomic regions to genomic annotations")
+ (description
+ "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
+differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
+to investigate the intersecting genomic annotations. Such annotations include
+those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
+CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
+enhancers. The annotatr package provides an easy way to summarize and
+visualize the intersection of genomic sites/regions with genomic
+annotations.")
+ (license license:gpl3)))
HCoop / jackhill / guix / guix.git / blobdiff